Description

Call variants from a BAM file using iVar

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

bam (file)

A sorted (with samtools sort) and trimmed (with iVar trim) bam file

*.bam

fasta (file)

The reference sequence used for mapping and generating the BAM file

*.fa

fai (file)

The index for the reference sequence used for mapping and generating the BAM file

*.fai

gff (file)

A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done.

save_mpileup (boolean)

Save mpileup file generated by ivar variants

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

tsv (file)

iVar generated TSV file with the variants

*.tsv

mpileup (file)

mpileup output from samtools mpileup [OPTIONAL]

*.mpileup

versions (file)

File containing software versions

versions.yml
included in
viralrecon
authors
Github user andersgs Github user drpatelh
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Tools

ivar
GPL-3.0-or-later

iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.

github.com/andersen-lab/ivar andersen-lab.github.io/ivar/html/manualpage.html